[Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1762


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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 Attachment #247 is|0                           |1
           obsolete|                            |
         AssignedTo|biopython-dev at biopython.org |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk
             Status|NEW                         |ASSIGNED




------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-21 10:13 -------
Created an attachment (id=252)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=252&action=view)
Bio/GenBank/__init__.py patch

Patches to my non-martel GenBank parser to:

(1) tackle the truncated LOCUS line problem (i.e. this bug)
(2) tackle missing features as in seqret output (i.e. this bug)

Plus a few changes that should be on bug 1899 really:

(3) started to split the feed function into sub functions
(4) minor changes to comments to remove references to Martel
(5) removed the ErrorParser class used by the Martel parser

And fix for bug 1903 as well:

(6) GenBank parses fails with unusual quoting and line breaks

The genbank unit test still works.

Michiel - could you create another (smaller) seqret file to go in the GenBank
unit tests?




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